Publications

2022
S. Sen, R.K. Kar, V.A. Borin, and I. Schapiro. 2022. “Insight into the isomerization mechanism of retinal proteins from hybrid quantum mechanics/molecular mechanics simulations.” Wiley Interdisciplinary Reviews: Computational Molecular Science, 12, 1. Publisher's Version Abstract
The photoisomerization of retinal is a unifying primary event in the rhodopsin protein family. In vertebrate rhodopsins it is the first step in the vision process, while in the microbial rhodopsins it activates the transport of ions across the cell-membrane. This reaction is highly optimized in the protein, which is ultrafast, selective, and efficient. A great effort was directed to elucidate the mechanism due to the overall complexity of the process inside the protein. The classical one-bond-flip is too demanding in space for the confined protein cavity. Therefore, various space saving mechanisms based on the rotation of multiple double bonds have been proposed. The hybrid quantum mechanics/molecular mechanics (QM/MM) method played an important role in the elucidation of the mechanism inside the tight protein environment. It allows to take the entire protein into account while describing the ground and excited states of retinal. The predicted mechanisms include full isomerization of two or three double bonds, a simultaneous isomerization of a single and a double bond as well as the partial rotation of bonds adjacent to the central isomerization. This review summarizes mechanistic studies in the literature and compares them. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Combined QM/MM Methods Software > Molecular Modeling. © 2021 Wiley Periodicals LLC.
F. Xin, L. Falsi, D. Pierangeli, F. Fusella, G. Perepelitsa, Y. Garcia, A.J. Agranat, and E. DelRe. 2022. “Intense wave formation from multiple soliton fusion and the role of extra dimensions.” Physical Review Letters, 129, 043901 .
A. Y. Strauss, A. Halaj, D. Zalaznik, I. Fradkin, B.A. Katz, E. Zlotnick, S. Barzilay, G.A. Anderson, D.D. Ebert, and J.D. Huppert. 2022. “Internet delivered guided cognitive behavioral self-help for panic disorder: An open trial and benchmarking study.” Journal of Behavioral and Cognitive Therapy, 32, Pp. 73-83.
Michaela Assouline and Sharon Gilad. 2022. “The Intersectionality of Deservingness for State Support.” Public Administration Review, 82, 3, Pp. 487-502.
Into the rabbit hole of discourse: Why studying text necessitates challenging concepts and methods
Christian Baden. 2022. “Into the rabbit hole of discourse: Why studying text necessitates challenging concepts and methods.” In YECREA Political Communication Preconference on "Advancing Concepts and Methods in Political Communication." Virtual Event.
O. Filiba, V.A. Borin, and I. Schapiro. 2022. “The involvement of triplet states in the isomerization of retinaloids.” Physical Chemistry Chemical Physics, 114, 1. Publisher's Version Abstract
Rhodopsins form a family of photoreceptor proteins which utilize the retinal chromophore for light energy conversion. Upon light absorption the retinal chromophore undergoes a photoisomerization. This reaction involves a non-radiative relaxation through a conical intersection between the singlet excited state and the ground state. In this work we studied the possible involvement of triplet states in the photoisomerization of retinaloids using the extended multistate (XMS) version of CASPT2. To this end, truncated models of three retinaloids were considered: protonated Schiff base, deprotonated Schiff base and the aldehyde form. The optimized geometries of the reactant, the product and the conical intersection were connected by a linear interpolation of internal coordinates to describe the isomerization. The energetic position of the low-lying singlet and triplet states as well as their spin-orbit coupling matrix elements (SOCME) were calculated along the isomerization profile. The SOCME values peaked in vicinity of the conical intersection for all the retinaloids. Furthermore, the magnitude of SOCME is invariant to the number of double bonds in the model. The SOCME for the protonated Schiff base is negligible (1.5 cm−1) which renders the involvement of the triplet state as improbable. However, the largest SOCME value of 30 cm−1 was found for the aldehyde form, followed by 15 cm−1 for the deprotonated Schiff base. © 2022 The Royal Society of Chemistry.
Sujoy Sarkar, Ajith C. Herath, Debdyuti Mukherjee, and Daniel Mandler. 2022. “Ionic strength induced local electrodeposition of ZnO nanoparticles.” ELECTROCHIMICA ACTA, 429.
Satoshi Takebayashi, Mark A. Iron, Moran Feller, Orestes Rivada-Wheelaghan, Gregory Leitus, Yael Diskin-Posner, Linda J. W. Shimon, Liat Avram, Raanan Carmieli, Sharon G. Wolf, Ilit Cohen-Ofri, Rajashekharayya A. Sanguramath, Roy Shenhar, Moris Eisen, and David Milstein. 2022. “Iron-catalysed ring-opening metathesis polymerization of olefins and mechanistic studies.” Nature Catalysis, 5, Pp. 494-502. DOI Abstract

The olefin metathesis reaction is among the most widely applicable catalytic reactions for carbon–carbon double bond formation. Currently, Mo– and Ru–carbene catalysts are the most common choices for this reaction. It has been suggested that an iron-based catalyst would be a desirable economical and biocompatible substitute of the Ru catalysts; however, practical solutions in this regard are still lacking. Here, we report the discovery and mechanistic studies of three-coordinate iron(II) catalysts for ring-opening metathesis polymerization of olefins. Remarkably, their reactivity enabled the formation of polynorbornene with stereoregularity and high molecular weight (>107 g mol–1). The polymerization in the presence of styrene revealed cross metathesis reactivity with iron catalysts. Mechanistic studies suggest the possible role of metal–ligand cooperation in formation of the productive catalyst. This work opens the door to the development of iron complexes that can be economical and biocompatible catalysts for olefin metathesis reactions.

J. Parravicini, E. DelRe, S. Perego, M. Acciarri, S. Binetti, Y. Garcia, G. Parapelitsa, A.J. Agranat, and G. Parravicini. 2022. “Key role of polar nanoregions in the cubic-to-tetragonal phase transition of potassium-based perovskites.” Phys. Rev B , 106, 064107.
Solomon O., Sapir H., Mervinetsky E., Chen Y.-J., Friedler A., and Yitzchaik S. 2022. “Kinase Sensing Based on Protein Interactions at the Catalytic Site.” Chem. Eur. J. Link Abstract

 

The role kinases play in regulating cellular processes makes them potential biomarkers for detecting the onset and prognosis of various diseases, including many types of cancer. Current kinase biosensors, including electrochemical and radiometric methods, rely on sensing the ATP-dependant enzymatic phosphorylation reaction. Here we introduce a new type of interaction-based electrochemical kinase biosensor that does not require any chemical labelling or modification. The basis for sensing is the interactions between the catalytic site of the kinase and the phosphorylation site of its substrate rather than the phosphorylation reaction. We demonstrated this concept with the ERK2 kinase and its substrate protein HDGF, which is involved in lung cancer. A peptide monolayer derived from the HDGF phosphorylation site was adsorbed onto a gold electrode and was used to sense ERK2 without ATP. The sensitivity of the assay was down to 10 nM of ERK2, corresponding with the range of its cellular concentrations. Surface chemistry analysis confirmed that ERK2 was bound to the HDGF peptide monolayer. This increased the permeability of redox-active species through the monolayer and resulted in ERK2 electrochemical sensing. Since our detection approach is based on protein-protein interactions and not on the enzymatic reaction, it can be further utilized for more selective detection of different types of enzymes.

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Maayan Shemer, Noam Greenbaum, Nimer Taha, Lena Brailovsky-Rokser, Yael Ebert, Ron Shaar, Christophe Falgueres, Pierre Voinchet, Naomi Porat, Galina Faershtein, and others. 2022. “Late Acheulian Jaljulia–Early human occupations in the paleo-landscape of the central coastal plain of Israel.” PloS one, 17, 5, Pp. e0267672.
Sharof Kurbanov, Abdurahmon Pulotov, and Firuz Aminov. 2022. ““Archaeological Excavations of Sanjar-Shah in 2016” (in Russian).” Arkheologicheskie raboty v Tadzhikistane, 42, Pp. 163-189.
sanjar2016.pdf
Sharof Kurbanov, Abdurahmon Pulotov, and Firuz Aminov. 2022. ““Archaeological Excavations of Sanjar-Shah in 2017” (in Russian).” Arkheologicheskie raboty v Tadzhikistane, 42, Pp. 163-189.
sanjar2017.pdf
Sharof Kurbanov, Abdurahmon Pulotov, and Firuz Aminov. 2022. ““Eastern Zaravshan Valley in the Early Islamic Period (8th-9th centuries): New Evidence from Sanjar-Shah Excavations (2016-2019)”.” In in Baumer Ch. and Novak, M. (eds.), Cultures in Contact Central Asia as Focus of Trade, Cultural Exchange and Knowledge Transmission, Pp. 327-351. Wiesbaden: Harrassowitz Verlag.
shenkar_kurbanov_pulotov_aminov_sanjar-shah.pdf
An “inverse” harpoon mechanism
Krishnendu Gope, Ester Livshits, Dror M. Bittner, Roi Baer, and Daniel Strasser. 2022. “An “inverse” harpoon mechanism.” Science Advances, 8, 39, Pp. eabq8084. Publisher's Version Abstract

Electron-transfer reactions are ubiquitous in chemistry and biology. The electrons quantum nature allows its transfer across long distances. In the well-known harpoon mechanism, electron-transfer results in Coulombic attraction between initially neutral reactants that leads to dramatic increase in the reaction rate. Here we present a different mechanism, in which electron-transfer from a neutral reactant to a multiply charged cation results in strong repulsion that encodes the electron-transfer distance in the kinetic energy release. 3D coincidence-imaging allows to identify such “inverse” harpoon products, predicted by non adiabatic molecular dynamics simulations to occur between H2 and HCOH2+ following double-ionization of isolated methanol molecules. Detailed comparison of measured and simulated data indicates that while the relative probability of long-range electron-transfer events is correctly predicted, theory overestimates the electron-transfer distance.

2022. ““The Arab Conquest and the Collapse of the Sogdian Civilization”.” In in Tor, D. and Inaba, M. (eds.), The History and Culture of Iran and Central Asia in the First Millennium CE: From the Pre-Islamic to the Islamic Era, Pp. 95-125. Notre Dame: Notre Dame University Press.
shenkar_the_arab_conquest_and_the_collapse.pdf
Sharon Gilad, Saar Alon-Barkat, Nitzan Faibish, and Sarah Goldberg. 2022. “Leveraging City Officials’ Professional and Social Identities to Facilitate Affordable Housing.” Political Geography , 94.
Limited Urban Citizenship: The Case of Community Councils in East Jerusalem
Nufar Avni, Noam Brenner, Dan Miodownik, and Gillad Rosen. 2022. “Limited Urban Citizenship: The Case of Community Councils in East Jerusalem.” Urban Geography, 43, 4, Pp. 546-566 . Publisher's Version Abstract

 

All around the world, urban spaces are disputed over issues of class, gender, ethnicity, and race. Urban citizenship within such spaces has been found to be fragmented, or even ‘dark.’ Intermediary organizations that represent spatially concentrated communities, such as Community Councils (CCs), often operate under these contentious circumstances. This paper focuses on the role of intermediary institutions in the contested city of (East) Jerusalem. We situate this case in the discussion on urban citizenship and highlight the precarity of the concept in a non-democratic context where most people are stateless residents. Building on in-depth interviews and site visits, we suggest that CCs implement a limited form of urban citizenship via a range of functions that vary from service provision to political representation. We explain the multifaceted nature of this limited urban citizenship and the process by which it is created, as well as its strengths and weaknesses. Through this case, we seek to enrich the literature on urban citizenship and CCs in contested cities with an emphasis on the multiple logics that operate in space, including the urban and the national.

 

Linear Weak Scalability of Density Functional Theory Calculations without Imposing Electron Localization
Marcel D. Fabian, Ben Shpiro, and Roi Baer. 2022. “Linear Weak Scalability of Density Functional Theory Calculations without Imposing Electron Localization.” J. Chem. Theory Comput., Pp. acs.jctc.1c00829. Publisher's Version Abstract

Linear scaling density functional theory (DFT) approaches to the electronic structure of materials are often based on the tendency of electrons to localize in large atomic and molecular systems. However, in many cases of actual interest, such as semiconductor nanocrystals, system sizes can reach a substantial extension before significant electron localization sets in, causing a considerable deviation from linear scaling. Herein, we address this class of systems by developing a massively parallel DFT approach which does not rely on electron localization and is formally quadratic scaling yet enables highly efficient linear wall-time complexity in the weak scalability regime. The method extends from the stochastic DFT approach described in Fabian et al. (WIRES: Comp. Mol. Sci. 2019, e1412) but is entirely deterministic. It uses standard quantum chemical atomcentered Gaussian basis sets to represent the electronic wave functions combined with Cartesian real-space grids for some operators and enables a fast solver for the Poisson equation. Our main conclusion is that when a processor-abundant high-performance computing (HPC) infrastructure is available, this type of approach has the potential to allow the study of large systems in regimes where quantum confinement or electron delocalization prevents linear scaling.

H. Dayan, M. Khoury-Kassabri, and Y. Pollak. 2022. “The link between ADHD symptoms and antisocial behavior: the moderating role of the protective factor sense of coherence.” Brain Sciences, 12, 10, Pp. 1336. Publisher's Version

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